UNIT 1 Taxonomy PDF

UNIT I. Introduction to Taxonomy OUTLINE 1. Define Taxonomy, Systematics, Phylogeny, Classification, Nomenclature, Description, and identification 2. What are the OBJECTIVES of Taxonomy/Systematics 3. What are the DUTIES of Taxonomists/Systematists 4. Cri...

UNIT I. Introduction to Taxonomy OUTLINE 1. Define Taxonomy, Systematics, Phylogeny, Classification, Nomenclature, Description, and identification 2. What are the OBJECTIVES of Taxonomy/Systematics 3. What are the DUTIES of Taxonomists/Systematists 4. Critical Problems & Opportunities of Taxonomists/Systematists Jennifer G. Opiso CMU-IBS, Plant Biology Division TAXONOMY A major part of systematics that includes four components: Description, Identification, Nomenclature, and Classification. The general subjects of study are taxa (singular, taxon), which are defined or delimited groups of organisms. Derived from the Greek word, 0 taxis (“arrangement”) and nomos (“law”) In 1735, Carl Linnaeus created a What rank share the hierarchical classification system fewest characters? SYSTEMATICS Defined as a science that includes and encompasses traditional taxonomy, the description, identification, nomenclature, and classification of organisms, and that has as its primary goal the reconstruction of phylogeny, or evolutionary history, of life. * It may utilize data from all fields of biology: morphology, anatomy, embryology/ development, ultrastructure, paleontology, ecology, geography, chemistry, physiology, genetics, karyology, and cell/molecular biology. What is Evolution? Evolution, means “change” and can be viewed as the cumulative changes occurring since the origin of the universe some 14 billion years ago. Biological evolution, the evolution of life, may be defined as “descent with modification.” (Charles Darwin) Descent is the transfer of genetic material (enclosed within a cell, the unit of life) from parent(s) to offspring over time.  Descent through time results in the formation of a lineage (Figure A and B), a set of organisms interconnected through time and space by the transfer of genetic material from parents to offspring. Taxonomy of higher Vascular Plants  TAXONOMIC COMPONENTS A. Description is the assignment of features or attributes to a taxon. The features are called characters. Two or more forms of a character are character states. Example of a character is “petal color,” for which two character states are “yellow” and “blue.” Another character is “leaf shape,” for which possible character states are “elliptic,” “lanceolate,” and “ovate.” * The purpose of these descriptive character and character state terms is to use them as tools of communication, for concisely categorizing and delimiting the attributes of a taxon, an organism, or some part of the organism. What CHARACTER is shown in the figure? What CHARACTER STATES is/are shown in the figure? B. Identification is the process of associating an unknown taxon with a known one, or recognizing that the unknown is new to science and warrants formal description and naming. * One generally identifies an unknown by first noting its characteristics, that is, by describing it. Then, these features are compared with those of other taxa to see if they conform. * A taxonomic key is perhaps the most utilized of identification devices. Of the different types of taxonomic keys, the most common, used in virtually all floras, is a dichotomous key. A dichotomous key consists of a series of two contrasting statements. Each statement is a lead; the pair of leads constitutes a couplet (Figure 1). That lead which best fits the specimen to be identified is selected; then all couplets hierarchically beneath that lead (by indentation and/or numbering) are sequentially checked for agreement until an identification is reached Figure 1. Dichotomous key to the genera of the Crassulaceae of California C. Nomenclature is the formal naming of taxa according to some standardized system. For plants, algae, and fungi, the rules and regulations for the naming of taxa are provided by the International Code of Botanical Nomenclature. These formal names are known as Scientific names, which by convention are translated into the Latin language. The fundamental principle of nomenclature is that all taxa may bear only one scientific name. The scientific name of a species traditionally consists of two parts (typically underlined or italicized): the genus name, which is always capitalized, e.g., Quercus, plus the specific epithet, which by general consensus is not capitalized, e.g., agrifolia. Thus, the species name for what is commonly called California live oak is Quercus agrifolia. Species names are known as binomials (literally meaning “two names”) and this type of nomenclature is called binomial nomenclature, first formalized in the mid-18th century by Carolus Linnaeus. D. Classification is the arrangement of entities (in this case, taxa) into some type of order. The purpose of classification is to provide a system for cataloguing and expressing relation- ships between these entities. Taxonomists have traditionally agreed upon a method for classifying organisms that utilizes categories called ranks. These taxonomic ranks are hierarchical, meaning that each rank is inclusive of all other ranks beneath it (Figure 1.8). A taxon is a group of organisms typically treated at a given rank. Thus, in the example of Figure 1.8, Magnoliophyta is a taxon placed at the rank of phylum Note that taxa of a particular rank generally end in a particular suffix. What taxon is placed at the rank of class? Araceae is placed at what rank? There are two major means of arriving at a classification of life: Phenetic classification is that based on overall similarities. Most of our everyday classifications are phenetic. Many traditional classifications in plant systematics are phenetic, based on noted similarities between and among taxa. Phylogenetic classification is that which is based on evolutionary history, or pattern of descent, which may or may not correspond to overall similarity PHYLOGENY Refers to the evolutionary history of a group of organisms. It is commonly represented in the form of a cladogram (or phylogenetic tree), a branching diagram that conceptually represents the evolutionary pattern of descent (see Figure). The lines of a cladogram represent lineages, which denote descent, the sequence of ancestral-descendant populations through time (Figure A). Thus, cladograms have an implied (relative) time scale. Any branching of the cladogram represents lineage divergence, the diversification of lineages from one common ancestor. cladograms serve as the basis for phylogenetic classification A monophyletic group, or clade, is a group consisting of a common ancestor plus all (and only all) descendants of that common ancestor. For example, the monophyletic groups of the cladogram in Figure B are circled. Cladogram with common ancestors shown and monophyletic groups (clades) circled. A phylogenetic classification recognizes only monophyletic groups. Note that some monophyletic groups are included within others (e.g., in Figure 1.9B the group containing only taxa E and F is included within the group containing only taxa D, E, and F, which is included within the group containing only taxa B, C, D, E, and F, etc.). The sequential listing of clades can serve as a phylogenetic classification scheme  Clades within clades A clade (also known as a monophyletic group) is a group of organisms that includes a single ancestor and all of its descendents. If you have to make more than one cut to separate a group of organisms from the rest of the tree, that group does not form a clade. Such non-clade groups are called either polyphyletic or paraphyletic groups depending on which taxa they include.  Cladogram showing lineages and apomorphies, the latter indicated by thick hash marks. Evolution may be recognized as a change from a preexisting, or ancestral, character state to a new, derived character state. The derived character state is an evolutionary novelty, also called an apomorphy Phylogenetic systematics, or cladistics, is a methodology for inferring the pattern of evolutionary history of a group of organisms, utilizing these apomorphies. Apomorphy unique to a given taxon is autapomorphy. Apomorphy shared by two or more taxa and inherited from a common ancestor is synapomorphy For example, the wings of ibirds and bats, which are all used for flying, are homoplastic (meaning: similar in form and structure, but not in origin).  Analogy vs Homology Homology indicates common ancestry. Homologous structures are those that share ancestry. Thus, the forelimb of a mouse and the wing of a bat are homologous structures, as the bat's wing is derived from the ancestral tetrapod forelimb. Analogy, on the other hand, implies common function but NOT from a common ancestor like the wings of a bat & a bird  ANALOGY vs HOMOPLASY A homoplasy is a character shared across clades in a phylogeny that don't share direct ancestry Homoplasy occurs when two different groups of organisms have a similar characteristic but are not derived from a common ancestor. EXAMPLE : Cell walls in plants and fungi, which are not closely related * Analogous structures are common traits found in different groups of species which are anatomically different, serve the same function, but evolved independently in the different groups of species. EXAMPLE: bird and bat wings are analogous as wings  HOMOLOGY vs HOMOPLASY Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. A homoplasy is a character shared across clades in a phylogeny that don't share direct ancestry Homoplasy occurs when two different groups of organisms have a similar characteristic but are not derived from a common ancestor. EXAMPLE : Cell walls in plants and fungi, which are not closely related * Analogous structures are common traits found in different groups of species which are anatomically different, serve the same function, but evolved independently in the different groups of species. EXAMPLE: bird and bat wings are analogous as wings HOMOPLASY vs HOMOLOGY Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. HOMOLOGY EXAMPLE  Understanding evolutionary relationships The key to understanding evolutionary How do relationships is common ancestry you tell which Common organisms ancestry refers on a tree to the fact that distinct are most descendent closely lineages have related to the same one ancestral lineage another? in common with one another To find the most recent common ancestor of a set of taxa on a phylogenetic tree, follow each taxon’s lineage back in time (towards the base of the tree) until all the lineages meet up Taxa that share a more recent common ancestor with one another are more closely related than are taxa whose most recent common ancestor is older. Because the triangle taxon shares a more recent common ancestor with the square taxon than either does with the star taxon, we can say that the triangle and square taxa are more closely related to one another than either is to the star taxon. Trees are hypotheses This example highlights a basic characteristic of evolutionary trees: they are hypotheses that have been tested with evidence. Because the discovery of new DNA evidence caused paleontologists to re-evaluate their interpretations of the fossil evidence, leading to a revision of our understanding of the evolutionary relationships in this group. Sister groups Outgroup Comprises the closest a more distantly related group of relative(s) of another given unit organisms that serves as a reference in an evolutionary tree. group when determining the evolutionary relationships of the ingroup Terminal taxon Polytomy A clade, species, or lineage represented as a node which that appears at the tip of a has more than two immediate phylogenetic tree. Terminal descending branches. taxa may be extant or extinct. Character state change Node Ingroup Root  Tips for tree reading Time runs from the root to The branching pattern of a tree the tips of a tree, not across indicates relatedness; taxa that its tips. share more recent common ancestors are more closely related. The circle and star taxa are adjacent to one another, but their most recent common ancestor is actually near the base of the tree. The star and rectangle taxa are actually much more closely related than the circle and star taxa are because the star’s and rectangle’s most recent common ancestor is younger and occurs nearer the tips of the tree!  Tips for tree reading Trees depict evolutionary relationships, not evolutionary progress.  It’s easy to think that taxa that appear near one side of a phylogenetic tree are more advanced than other organisms on the tree, but this is simply not the case. First, the idea of evolutionary “advancement” is not a particularly scientific idea. There is no unbiased, universal scale for “advancement.” Second, taxa with extreme versions of traits (which might be perceived as more “advanced”) may occur on any terminal branch. The position of a terminal taxon is not an indication of how adaptive, specialized, or extreme its traits are.  Branch rotation It’s possible to rotate branches around nodes without changing the evolutionary relationships depicted This has the effect of changing the order of terminal taxa, but not changing the information that the tree conveys. Do these trees tell the same story?  OBJECTIVES OF SYSTEMATICS To prepare a scheme of classification that provides phenetic, natural or phylogenetic relationships among plants To establish a suitable method for identification, nomenclature, and description of plant taxa To assign each taxon a name following internationally accepted rules (International Botanical Congress) To provide an inventory of plant taxa To create an understanding of the evolutionary process To train the students in regard to the diversity of organisms & their relationship with other biological branches  DUTIES OF TAXONOMISTS Conduct research on classification systems and taxonomic classifications Identify, describe, and classify organisms according to established taxonomic criteria Develop and maintain databases of specimens and information related to taxonomy Identify & analyze relationships between organisms and their environment Develop & implement strategies for collecting & preserving specimens Develop & maintain taxonomic keys to identify species Collaborate with researchers to identify research needs Write and publish scientific papers & reports Conduct research on classification systems and taxonomic classifications Mt. Apo Mt. Kitanglad Mt. Arayat Mt. Hamiguitan Mt. Pinatubo  Collaborate with researchers to identify research needs * National Science Foundation, USA & Fort Worth Botanic Gardens (FWBG)/ Botanical Research Institute of Texas (BRIT) through the Principal Invesigator, Dr. Peter W. Fritsch and Co-P.I., Dr. Manuela Dal Forno * California Academy of Sciences (CAS) through Dr. James Shevock * University of North Carolina- Wilmington through Dr. Darin Penneys * Missouri Botanical Garden through Dr. John Brinda * Botanischer Garten und Botanisches Museum, Berlin through Dr. Bibiana Moncada * Bartlett Tree Research Laboratories and Arboretum through Sir Adam Black for the conservation initiatives  OPPORTUNITIES OF A TAXONOMIST 1. School and College professors 2.Researchers and Scientists 3.Landscaping artists (plants background or plant taxonomy background can be helpful in diversifying plant choice) 4. Horticulturalists 5. Plant consultants for big corporations ( e.g. plant-based industries and plant pharmaceutical firms) 6. Forest officers and policy makers 7. Environmentalists and NGOs working with tropical forests and their indigenous inhabitants 8. Interdisciplinary research roles in companies (working both with plant and animal life)  CRITICAL PROBLEMS CONCERNING TAXONOMY Gaps in taxonomic knowledge, a lack of taxonomic infrastructure, and an insufficient number of experts; together these are called the “taxonomic impediment” The lack of association between sequences and taxonomic names, whether due to misidentification, lack of comparison with morphologically described species, or simply not assigning a name, is a problem that needs to be addressed and systematized in order to achieve reliability in the use of databases. many species are being described poorly in isolated publications, with no attempt to relate a new taxon to existing species and classifications. Many of these 'new' species will have been described before, so sorting out the mess will be the headache of the next generation of taxonomists. CRITICAL PROBLEMS CONCERNING TAXONOMY Species are always changing. As a consequence, they are essentially only a somewhat arbitrarily defined point along an evolutionary line. The major limitation of the Linnaean classification system is that it is based on physical traits. Physical traits may not necessarily be a sign of relatedness and indeed DNA evidence has forced scientists to reconsider many classifications based on the old system. the lack of trained taxonomists and inadequate funding for taxonomic research pose significant challenges to the field (Sharma et al., 2017). Thank You for listening